ARTICLE IN PRESS Molecular Phylogenetics and Evolution xxx (2008) xxx–xxx Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenetic relationships of Ruteae (Rutaceae): New evidence from the chloroplast genome and comparisons with non-molecular data Gabriele Salvo a,*, Gianluigi Bacchetta b, Farrokh Ghahremaninejad c, Elena Conti a a Institute of Systematic Botany, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland b Center for Conservation of Biodiversity (CCB), Department of Botany, University of Cagliari, Viale S. Ignazio da Laconi 13, 09123 Cagliari, Italy c Department of Biology, Tarbiat Moallem University, 49 Dr. Mofatteh Avenue, 15614 Tehran, Iran article info abstract Article history: Phylogenetic analyses of three cpDNA markers (matK, rpl16, and trnL–trnF) were performed to evaluate Received 12 December 2007 previous treatments of Ruteae based on morphology and phytochemistry that contradicted each other, Revised 14 July 2008 especially regarding the taxonomic status of Haplophyllum and Dictamnus. Trees derived from morpho- Accepted 9 September 2008 logical, phytochemical, and molecular datasets of Ruteae were then compared to look for possible pat- Available online xxxx terns of agreement among them. Furthermore, non-molecular characters were mapped on the molecular phylogeny to identify uniquely derived states and patterns of homoplasy in the morphological Keywords: and phytochemical datasets. The phylogenetic analyses determined that Haplophyllum and Ruta form Ruta reciprocally exclusive monophyletic groups and that Dictamnus is not closely related to the other genera Citrus family Morphology of Ruteae. The different types of datasets were partly incongruent with each other. The discordant phy- Phytochemistry logenetic patterns between the phytochemical and molecular trees might be best explained in terms of Congruence convergence in secondary chemical compounds. Finally, only a few non-molecular synapomorphies pro- Shimodaira–Hasegawa test vided support for the clades of the molecular tree, while most of the morphological characters tradition- Character mapping ally used for taxonomic purposes were found to be homoplasious. Within the context of the phylogenetic Homoplasy relationships supported by molecular data, Ruta, the type genus for the family, can only be diagnosed by using a combination of plesiomorphic, homoplasious, and autapomorphic morphological character states. Ó 2008 Elsevier Inc. All rights reserved. 1. Introduction More generally, the choice of characters for phylogenetic analy- sis has been a crucial and controversial issue in systematics (e.g., Testing whether traditional taxonomic classifications based on Hart et al., 2004; Stace, 2005) and the relative role of molecular morphology are congruent with more recent molecular phyloge- and morphological data in reconstructing phylogenies has been netic findings has become a central task in the current systematic extensively debated (Hillis, 1987; Patterson, 1988; Sytsma, 1990; agenda (e.g., Simões et al., 2004; Van der Niet et al., 2005; Wiens Donoghue and Sanderson, 1992; Novacek, 1994; Baker et al., et al., 2005; Marazzi et al., 2006; Rønsted et al., 2007; but see 1998; Wahlberg and Nylin, 2003; Wortley and Scotland, 2006). Di- Grant, 2003). Disagreements between morphological taxonomies rectly linked to character choice is the controversy about combined and molecular phylogenies have often been attributed to high lev- versus separate analyses of different datasets (Bull et al., 1993; de els of homoplasy in characters traditionally used to delimit taxa Queiroz et al., 1995). For example, should morphological, molecu- (e.g., Lavin et al., 2001; Moylan et al., 2004; Mueller et al., 2004; Si- lar, and phytochemical characters for a certain group of organisms mões et al., 2006) and taxon diagnoses based on plesiomorphic be analyzed together or separately? Advocates of separate analyses morphological character-states (e.g., Roalson et al., 2005; Norup have stressed the fact that congruence among trees derived from et al., 2006). Incongruence between molecular phylogenies and independent sources of data can offer strong evidence for the accu- morphological classifications has prompted the recognition of racy of the inferred relationships (Swofford, 1991; Hillis, 1995; groups highly supported by molecular data, but lacking unique Miyamoto and Fitch, 1995; Graham et al., 1998), while incongru- morphological synapomorphies (e.g., Porter and Johnson, 2000; ence can provide initial insights on important biological phenom- Lavin et al., 2001; Hughes et al., 2004), or the dismantling of tradi- ena, ranging from hybridization to lineage sorting (e.g., Rieseberg tionally accepted taxa (e.g., Kim et al., 1996; Kron et al., 1999; et al., 1996; Won and Renner, 2003; Doyle et al., 2004). Conversely, Wiens et al., 2005). advocates of global evidence have emphasized the fact that com- bining datasets before phylogenetic analysis grants the best oppor- * Corresponding author. Fax: +41 446348403. tunity to resolve relationships at different scales of divergence E-mail address: [email protected] (G. Salvo). (Cunningham, 1997; Kluge, 1998; Gatesy and Baker, 2005). 1055-7903/$ - see front matter Ó 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2008.09.004 Please cite this article in press as: Salvo, G. et al., Phylogenetic relationships of Ruteae (Rutaceae): New evidence from ..., Mol. Phylogenet. Evol. (2008), doi:10.1016/j.ympev.2008.09.004 ARTICLE IN PRESS 2 G. Salvo et al. / Molecular Phylogenetics and Evolution xxx (2008) xxx–xxx Ruta L. (Rutaceae Juss.) and related genera offer a primary Ruta (around 60 species) by tetra- and pentamerous flowers, a example of the discordant systematic conclusions that can be thick cushion-shaped nectary disk, and dorsally angled seeds; reached by using different types of data. Below we provide the nec- Thamnosma (one species) by almost reniform seeds and variation essary background to understand the sources of such discrepancy in the shape of the nectary disk; Boenninghausenia (one species) and explain how novel evidence from molecular characters might by a cup-shaped nectary disk and filiform filaments; Cneoridium help to clarify the discordant taxonomic treatments published un- (one species) by one carpel, two ovules per locule, and an almost til now. The paucity of diagnostic morphological traits, combined spherical stigma; Psilopeganum (one species) by a relatively small with their overlapping and contradicting nature, has hindered both nectary disk with a narrow ending; and Dictamnus (one species) a stable circumscription for Ruta—alternately subjected to taxo- by zygomorphic flowers, lanceolate petals and sepals, club-shaped nomic ‘‘lumping” (Engler, 1896, 1931) and ‘‘splitting” (Townsend, filaments with protruding glands, and three ovules per locule (see 1968, 1986)—and the unequivocal identification of relationships Table 2). Psilopeganum was analyzed in a systematic context only with other genera of Rutaceae (Townsend, 1986). by Engler (1896, 1931), but its narrow occurrence in the Three At the family level, Rutaceae (161 genera/1815 species; Stevens, Gorges Reservoir area of central China (Song et al., 2004; Tang 2001 onwards, Angiosperm Phylogeny Website) have been investi- et al., 2007) prevented its inclusion in more recent taxonomic gated morphologically (Engler, 1896, 1931; Saunders, 1934; treatments (e.g., Townsend, 1986; Da Silva et al., 1988). Moore, 1936; Scholz, 1964; Tilak and Nene, 1978), molecularly Despite the systematic importance of the above-mentioned (Chase et al., 1999; Scott et al., 2000; Samuel et al., 2001; Morton diagnostic features, relationships and taxonomic boundaries et al., 2003), and biochemically, owing to their remarkable diver- among the six genera of Ruteae (Engler, 1896, 1931) remain con- sity of secondary chemical compounds (Price, 1963; Fish and troversial. Townsend (1986) observed that the states of some char- Waterman, 1973; Waterman 1975, 1983, 1990; Gray and Water- acters traditionally used to differentiate the genera overlap or man, 1978; Waterman and Grundon, 1983; Kong et al., 1986; Ng suggest contradicting sister-group relationships (Table 2). For et al., 1987; Da Silva et al., 1988; Zakaria, 2001). However, different example, the ranges of the number of ovules per locule overlap types of characters led to contrasting systematic conclusions. For across Ruta and allied genera. The presence of cuneate filaments fa- example, some taxonomic groups recognized in the most compre- vors Cneoridium and Thamnosma as sister taxa, whereas spherical hensive morphological study (Engler, 1896, 1931) and the most re- seeds link Cneoridium with Dictamnus. Moreover, Townsend cent chemotaxonomic survey (Da Silva et al., 1988) of Rutaceae (1986) argued that there are no grounds for considering Haplophyl- conflict with each other and with the groups supported in the lum to be more closely related to Ruta than to Thamnosma, as pro- broadest molecular phylogenies available until now (Chase et al., posed by Engler (1896, 1931). In fact, while Ruta and Haplophyllum 1999; Scott et al., 2000). The cited molecular studies, based on share several morphological similarities, including translucent dots sparse character and taxon sampling, supported Ruta either as sis- on the leaves, yellowish flowers, a thick nectary disk, a short thick ter to a genus of subfamily Flindersioideae (Chase et al.,